3D structure for Adenylate-3'-phosphate-[[2'-deoxy-uridine-5'-phosphate]-3'-phosphate] (DB03186)

448108
  -OEChem-11151917383D

77 81  0     1  0  0  0  0  0999 V2000
    0.1397    3.3460   -2.0570 P   0  0  1  0  0  0  0  0  0  0  0  0
   -7.2850    0.3112    0.4468 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6017    4.0096    0.2198 P   0  0  2  0  0  0  0  0  0  0  0  0
    1.7775   -1.9523   -3.8219 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0177   -0.0499   -0.2111 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3678    0.5656    0.4401 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9067   -0.5030    0.6527 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4908   -1.9986    2.4259 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4226    3.0237   -1.1209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4888    2.7095   -0.1543 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4712   -0.7215   -2.8166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7929    4.3041   -1.1484 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7116    4.3506   -3.1888 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2643   -0.8088   -0.1868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8536    0.4955    1.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4552    3.4285    1.2021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5653    2.1372   -2.6011 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1659    1.5751   -0.3538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3635    5.1842    0.7602 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1847    2.8898    2.3217 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3384   -1.7394   -4.1870 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7957   -3.2456   -2.8512 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8578   -2.0499   -5.0038 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8490   -0.8512    2.7109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7557   -1.7775    0.8153 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5574    0.9596    1.1649 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3446   -1.8686    1.5572 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8903   -3.9211   -0.3194 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5106    1.0261    2.5137 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2129   -5.1474   -0.1493 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1178   -4.2768    1.0085 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8291    0.1543    1.3199 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8528   -0.8803    1.8437 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9907    0.8983    0.2851 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0986   -1.2534    0.5765 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3169    1.9693   -1.4698 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8184    0.6535   -0.8888 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6410    2.1723   -0.7706 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3867    1.5630    0.5986 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2452    2.0893    0.8707 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2967   -0.5604   -1.6746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580   -2.9780    0.3951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7561   -1.1474    1.5081 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0449   -3.0153    0.8656 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3949    1.7137    2.0178 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8633   -0.3632    0.8729 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7882   -4.1535    0.5696 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9304   -1.0051    1.3532 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8585   -0.2900    2.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0716   -4.9720   -0.5434 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2319    0.7913    2.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1953   -0.4252    2.5928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5734    1.2186   -0.5841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6456   -2.0032   -0.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4232    1.9550   -2.5593 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7277    0.6358   -0.7946 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9450    3.2209   -0.6934 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4309    1.6296   -1.3037 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9894    2.3236    1.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5560    1.7738    1.6602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9499    2.8179    1.2841 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2207   -1.4586   -1.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3423   -0.4562   -1.9806 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0548   -1.6697    3.1464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8777   -0.1663    1.9464 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2001   -0.9004    0.2101 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1280    1.5479    3.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1404   -2.0374    1.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1379    4.5838   -3.9495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1556   -0.5398   -0.4957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6692    1.0227    2.0867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4996   -5.7869   -1.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0924    2.6732    0.8988 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5508   -3.5343    1.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6379   -5.1128    0.7792 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7500   -2.3158   -4.8655 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8963   -4.1367   -3.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  1 17  2  0  0  0  0
  2  7  1  0  0  0  0
  2 14  1  0  0  0  0
  2 15  1  0  0  0  0
  2 18  2  0  0  0  0
  3 10  1  0  0  0  0
  3 12  1  0  0  0  0
  3 16  1  0  0  0  0
  3 19  2  0  0  0  0
  4 11  1  0  0  0  0
  4 21  1  0  0  0  0
  4 22  1  0  0  0  0
  4 23  2  0  0  0  0
  5 34  1  0  0  0  0
  5 35  1  0  0  0  0
  6 37  1  0  0  0  0
  6 39  1  0  0  0  0
  7 32  1  0  0  0  0
  8 33  1  0  0  0  0
  8 64  1  0  0  0  0
  9 36  1  0  0  0  0
 10 40  1  0  0  0  0
 11 41  1  0  0  0  0
 13 69  1  0  0  0  0
 14 70  1  0  0  0  0
 15 71  1  0  0  0  0
 16 73  1  0  0  0  0
 20 45  2  0  0  0  0
 21 76  1  0  0  0  0
 22 77  1  0  0  0  0
 24 49  2  0  0  0  0
 25 35  1  0  0  0  0
 25 42  1  0  0  0  0
 25 43  1  0  0  0  0
 26 39  1  0  0  0  0
 26 45  1  0  0  0  0
 26 46  1  0  0  0  0
 27 43  2  0  0  0  0
 27 44  1  0  0  0  0
 28 42  2  0  0  0  0
 28 50  1  0  0  0  0
 29 45  1  0  0  0  0
 29 49  1  0  0  0  0
 29 67  1  0  0  0  0
 30 47  1  0  0  0  0
 30 50  2  0  0  0  0
 31 47  1  0  0  0  0
 31 74  1  0  0  0  0
 31 75  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 32 51  1  0  0  0  0
 33 35  1  0  0  0  0
 33 52  1  0  0  0  0
 34 40  1  0  0  0  0
 34 53  1  0  0  0  0
 35 54  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 36 55  1  0  0  0  0
 37 41  1  0  0  0  0
 37 56  1  0  0  0  0
 38 39  1  0  0  0  0
 38 57  1  0  0  0  0
 38 58  1  0  0  0  0
 39 59  1  0  0  0  0
 40 60  1  0  0  0  0
 40 61  1  0  0  0  0
 41 62  1  0  0  0  0
 41 63  1  0  0  0  0
 42 44  1  0  0  0  0
 43 65  1  0  0  0  0
 44 47  2  0  0  0  0
 46 48  2  0  0  0  0
 46 66  1  0  0  0  0
 48 49  1  0  0  0  0
 48 68  1  0  0  0  0
 50 72  1  0  0  0  0
M  END
> <DATABASE_ID>
DB03186

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/JIAJERGOUFOENU-LNAOLWRRSA-N/SDF?record_type=3d

> <SMILES>
[H]N([H])C1=C2N=CN([C@@H]3O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]4C[C@@H](O[C@@H]4COP(O)(O)=O)N4C=CC(=O)N([H])C4=O)[C@@H](OP(O)(O)=O)[C@H]3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C19H27N7O20P4/c20-16-13-17(22-6-21-16)26(7-23-13)18-14(28)15(45-48(33,34)35)10(43-18)5-41-49(36,37)46-50(38,39)44-8-3-12(25-2-1-11(27)24-19(25)29)42-9(8)4-40-47(30,31)32/h1-2,6-10,12,14-15,18,28H,3-5H2,(H,36,37)(H,38,39)(H2,20,21,22)(H,24,27,29)(H2,30,31,32)(H2,33,34,35)/t8-,9+,10+,12+,14+,15+,18+/m0/s1

> <INCHI_KEY>
JIAJERGOUFOENU-LNAOLWRRSA-N

> <FORMULA>
C19H27N7O20P4

> <MOLECULAR_WEIGHT>
797.3476

> <EXACT_MASS>
797.026132387

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
62.791481251120786

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-2-[({[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-2-[(phosphonooxy)methyl]oxolan-3-yl]oxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-4-hydroxyoxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-0.57

> <JCHEM_LOGP>
-6.0207191440001635

> <ALOGPS_LOGS>
-2.19

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
1.2846260123609017

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.6760845885768297

> <JCHEM_PKA_STRONGEST_BASIC>
3.9993586153350904

> <JCHEM_POLAR_SURFACE_AREA>
393.5299999999999

> <JCHEM_REFRACTIVITY>
153.9631

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.12e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R)-2-(4-aminobutanamido)-3-{[(4-methoxyphenyl)methyl]sulfanyl}propanamido]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for Adenylate-3'-phosphate-[[2'-deoxy-uridine-5'-phosphate]-3'-phosphate] (DB03186)

Structure for Adenylate-3'-phosphate-[[2'-deoxy-uridine-5'-phosphate]-3'-phosphate] (DB03186)